Alignments for a candidate for ilvI in Clostridium tyrobutyricum FAM22553

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvI in Clostridium tyrobutyricum FAM22553

Align acetohydroxy-acid synthase large subunit (EC 2.2.1.6) (characterized)
to candidate WP_039651790.1 PN53_RS01910 biosynthetic-type acetolactate synthase large subunit

Query= metacyc::MONOMER-11900
         (599 letters)



>NCBI__GCF_000816635.1:WP_039651790.1
          Length = 536

 Score =  491 bits (1263), Expect = e-143
 Identities = 263/557 (47%), Positives = 362/557 (64%), Gaps = 30/557 (5%)

Query: 1   MNGAEAMIKALEAEKVEILFGYPGGALLPFYDALHHSDLIHLLTRHEQAAAHAADGYARA 60
           M  AEA+I+ L+ E+V ++FGYPG A++P Y+AL  SD+ H+L R EQAA H+A GYAR+
Sbjct: 1   MKAAEAIIQYLKKEEVNMVFGYPGAAVVPIYEALRKSDIKHVLVRQEQAAGHSASGYARS 60

Query: 61  SGKVGVCIGTSGPGATNLVTGVATAHSDSSPMVALTGQVPTKLIGNDAFQEIDALGLFMP 120
           +GKVGVCI TSGPGATNL+TG+A+A+ DS PMV +TGQV + LIG D FQE+D  G    
Sbjct: 61  TGKVGVCIVTSGPGATNLITGIASAYMDSIPMVIITGQVKSTLIGRDVFQELDITGATES 120

Query: 121 IVKHNFQIQKTCQIPEIFRSAFEIAQTGRPGPVHIDLPKDVQELELDIDKHPIPSKVKLI 180
             K++F ++++  IP+  + AF IA TGR GPV +D+P D+ E ++D      P  V + 
Sbjct: 121 FTKYSFLVRESKFIPKTIKEAFYIANTGRKGPVLVDIPVDIMEEDIDF---KYPEVVNIR 177

Query: 181 GYNPTTIGHPRQIKKAIKLIASAKRPIILAGGGVLLSGANEELLKLVELLNIPVCTTLMG 240
           GY PTT GH  QI+K I+ I ++KRPII AGGGV+L+ A  +L + VE  NIPV  TLMG
Sbjct: 178 GYKPTTKGHIGQIRKIIERIKTSKRPIICAGGGVILAKAENKLREFVEKSNIPVVHTLMG 237

Query: 241 KGCISENHPLALGMVGMHGTKPANYCLSESDVLISIGCRFSDRITGDIKSFATNAKIIHI 300
           KG I+E+    +G++G HG   AN  +  +DVLI IG R +DR T  IK FA NA +IHI
Sbjct: 238 KGSINEDSNYYVGLIGTHGFDYANKAVDNADVLILIGARATDRTTRGIKDFAKNADVIHI 297

Query: 301 DIDPAEIGKNVNVDVPIVGDAKLILKEVIKQLDYIINKDSKENNDKENISQWIENVNSLK 360
           DIDPAEIGKN+   +P+VGD + +L ++IK++  I         D EN   WI  +  + 
Sbjct: 298 DIDPAEIGKNLETFIPVVGDIENVLSKLIKEITPI---------DTEN---WINQIR-IW 344

Query: 361 KSSIPVMDYDDIPIKPQKIVKELMAVIDDLNINKNTIITTDVGQNQMWMAHYFKTQTPRS 420
           K+SI +       I P+  +  +   +D+      +I+ TDVGQNQ+W A  FK    R 
Sbjct: 345 KNSIEINKNPTDKINPRYALNNVSKKLDE-----ESILITDVGQNQIWCARNFKIMGNRK 399

Query: 421 FLSSGGLGTMGFGFPSAIGAKVAKPDSKVICITGDGGFMMNCQELGTIAEYNIPVVICIF 480
           FL+SGGLGTMG+  P+AIGAK+  PD  VI + GD GF M+  ELGT+ EY++ +V+ IF
Sbjct: 400 FLTSGGLGTMGYSIPAAIGAKMGCPDKNVIAVAGDAGFQMSLFELGTVKEYDVNIVMIIF 459

Query: 481 DNRTLGMVYQWQNLFYGKRQC----SVNFGGAPDFIKLAESYGIKARRIESPNEINEALK 536
           +N  LGMV + Q+     ++C     VNF   PDF+KLAESYGI A R+E  +E     +
Sbjct: 460 NNLGLGMVREIQD-----KKCEGEFGVNFKTNPDFVKLAESYGICAERVEKDDEFETVFE 514

Query: 537 EAINCDEPYLLDFAIDP 553
           +A+N D  +L++  +DP
Sbjct: 515 KALNSDRAFLIECVVDP 531


Lambda     K      H
   0.319    0.137    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 817
Number of extensions: 45
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 599
Length of database: 536
Length adjustment: 36
Effective length of query: 563
Effective length of database: 500
Effective search space:   281500
Effective search space used:   281500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_039651790.1 PN53_RS01910 (biosynthetic-type acetolactate synthase large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00118.hmm
# target sequence database:        /tmp/gapView.2802739.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00118  [M=557]
Accession:   TIGR00118
Description: acolac_lg: acetolactate synthase, large subunit, biosynthetic type
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-210  685.6   2.2   2.7e-210  685.5   2.2    1.0  1  NCBI__GCF_000816635.1:WP_039651790.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000816635.1:WP_039651790.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  685.5   2.2  2.7e-210  2.7e-210       1     539 [.       1     534 [.       1     536 [] 0.98

  Alignments for each domain:
  == domain 1  score: 685.5 bits;  conditional E-value: 2.7e-210
                             TIGR00118   1 lkgaeilveslkkegvetvfGyPGGavlpiydalydselehilvrheqaaahaadGyarasGkvGvvlatsGP 73 
                                           +k+ae++++ lkke+v++vfGyPG av+piy+al +s+++h+lvr eqaa h a Gyar++GkvGv+++tsGP
  NCBI__GCF_000816635.1:WP_039651790.1   1 MKAAEAIIQYLKKEEVNMVFGYPGAAVVPIYEALRKSDIKHVLVRQEQAAGHSASGYARSTGKVGVCIVTSGP 73 
                                           799********************************************************************** PP

                             TIGR00118  74 GatnlvtgiatayldsvPlvvltGqvatsliGsdafqeidilGitlpvtkhsflvkkaedlpeilkeafeias 146
                                           Gatnl+tgia+ay+ds+P+v++tGqv+++liG d fqe+di+G t + tk+sflv++++ +p+++keaf+ia+
  NCBI__GCF_000816635.1:WP_039651790.1  74 GATNLITGIASAYMDSIPMVIITGQVKSTLIGRDVFQELDITGATESFTKYSFLVRESKFIPKTIKEAFYIAN 146
                                           ************************************************************************* PP

                             TIGR00118 147 tGrPGPvlvdlPkdvteaeieleveekvelpgykptvkghklqikkaleliekakkPvllvGgGviiaeasee 219
                                           tGr GPvlvd+P d++e++i+++++e v+++gykpt+kgh  qi+k++e i+++k+P++ +GgGvi a+a+++
  NCBI__GCF_000816635.1:WP_039651790.1 147 TGRKGPVLVDIPVDIMEEDIDFKYPEVVNIRGYKPTTKGHIGQIRKIIERIKTSKRPIICAGGGVILAKAENK 219
                                           ************************************************************************* PP

                             TIGR00118 220 lkelaerlkipvtttllGlGafpedhplalgmlGmhGtkeanlavseadlliavGarfddrvtgnlakfapea 292
                                           l+e++e+ +ipv++tl+G+G+++ed +  +g++G hG  +an av++ad+li +Gar  dr+t  ++ fa++a
  NCBI__GCF_000816635.1:WP_039651790.1 220 LREFVEKSNIPVVHTLMGKGSINEDSNYYVGLIGTHGFDYANKAVDNADVLILIGARATDRTTRGIKDFAKNA 292
                                           ************************************************************************* PP

                             TIGR00118 293 kiihididPaeigknvkvdipivGdakkvleellkklkeeekkekeWlekieewkkeyilkldeeeesikPqk 365
                                            +ihididPaeigkn+++ ip+vGd ++vl++l+k+++  ++++  W+++i+ wk++  +  ++  ++i+P++
  NCBI__GCF_000816635.1:WP_039651790.1 293 DVIHIDIDPAEIGKNLETFIPVVGDIENVLSKLIKEITPIDTEN--WINQIRIWKNSIEI-NKNPTDKINPRY 362
                                           *************************************9998777..*********98764.5667789***** PP

                             TIGR00118 366 vikelskllkdeaivttdvGqhqmwaaqfyktkkprkfitsgGlGtmGfGlPaalGakvakpeetvvavtGdg 438
                                            ++++sk l++e+i+ tdvGq+q+w a+ +k+   rkf+tsgGlGtmG+ +Paa+Gak++ p+++v+av+Gd+
  NCBI__GCF_000816635.1:WP_039651790.1 363 ALNNVSKKLDEESILITDVGQNQIWCARNFKIMGNRKFLTSGGLGTMGYSIPAAIGAKMGCPDKNVIAVAGDA 435
                                           ************************************************************************* PP

                             TIGR00118 439 sfqmnlqelstiveydipvkivilnnellGmvkqWqelfyeerysetklaselpdfvklaeayGvkgiriekp 511
                                           +fqm+l el t++eyd++++++i+nn  lGmv+  q+   e+ +     +  +pdfvklae+yG+ ++r+ek+
  NCBI__GCF_000816635.1:WP_039651790.1 436 GFQMSLFELGTVKEYDVNIVMIIFNNLGLGMVREIQDKKCEGEFGVNFKT--NPDFVKLAESYGICAERVEKD 506
                                           **************************************999988765555..6******************** PP

                             TIGR00118 512 eeleeklkealeskepvlldvevdkeee 539
                                           +e e  +++al+s++  l++ +vd +e+
  NCBI__GCF_000816635.1:WP_039651790.1 507 DEFETVFEKALNSDRAFLIECVVDPHES 534
                                           ************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (557 nodes)
Target sequences:                          1  (536 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 15.53
//
[ok]

This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis